<tool id="igblastmerge" name="IgBlastMerge" version="1.0">
	<description>Multisample</description>
	<command interpreter="python">
		igblastmergems.py 
		--input
		#for $i, $f in enumerate($patients)
            $f.id
            #for $j, $g in enumerate($f.samples)
            	${g.sample}
            #end for

		#end for
		--output $out_file
	</command>
	<inputs>
		<repeat name="patients" title="Patients" min="1" default="1">
            <repeat name="samples" title="Sample" min="1" default="1">
                <param name="sample" format="tabular" type="data" label="Sample to Process" />
            </repeat>
			<param name="id" type="text" label="ID" />
		</repeat>
	</inputs>
	<outputs>
		<data format="tabular" name="out_file" />
	</outputs>
	<help>
		Step 3 of the Immune Repertoire tools, merges the parsed reports generated in step 2 into one file with an Sample ID.
	</help>

</tool>